[11-II-2013]
Hi Lachele,
Thank you very much for your help. I didn't really assumed that the atom names would be the correspondent atoms in Glycam. I just submitted the question just in case. I will email Carlos Simmerling as you suggest.
Thank you!!
Kepa K.
*******************************************
________________________________
De: Lachele Foley (Lists) <lf.list.gmail.com>
Para: Kepa K. Burusco <kekoburgo.yahoo.es>; AMBER Mailing List <amber.ambermd.org>
Enviado: Lunes 11 de febrero de 2013 20:01
Asunto: Re: [AMBER] Hydrogens AMBER 1H6 and 2H6 vs. Glycam H61 and H62 for Glucose
I think you should not assume that the numbering corresponds. Maybe
Carlos can help answer this, but that paper was published quite a
while ago.
On Mon, Feb 11, 2013 at 9:47 AM, Lachele Foley (Lists)
<lf.list.gmail.com> wrote:
> I'll have to do a little digging to answer questions about something
> from 1998. Be patient.
>
>
> On Mon, Feb 11, 2013 at 8:48 AM, Kepa K. Burusco <kekoburgo.yahoo.es> wrote:
>> [11-II-2013]
>>
>> Hi everybody,
>>
>> I apologise for submiting the question to the general amber users list, but by doing this maybe I get a bigger audience between people working with carbohydrates.
>>
>> I am planning to run some tests using the RESP set of charges for glucose anomers that were derived in the paper:
>>
>> "Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the alpha => beta Anomerization of Glucose"
>>
>> J. Am. Chem. Soc. 1998, 120, 5771-5782.
>>
>> The charges are available for alpha and beta anomers in Table 1, but only a few atom names are shown in Figure 1.
>>
>> As can be seen, the charges for 1H6 and 2H6 (H61 and H62 in Glycam06h) are different but I cannot identify which is which in the 3D structure. This point was not important in Glycam06 because H61 and H62 have charge = 0.00 but it's not the case now and I would need to know to correctly assign the right charge to the right Hydrogen atom.
>>
>> Can I assume that 1H6 and 2H6 names in the paper are in agreement to Glycam06 atom names H61 and H62?
>>
>>
>> Any help will be welcome.
>>
>> Thank you very much.
>>
>> Kepa K.
>>
>> ************************************************
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>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Feb 11 2013 - 13:00:03 PST
